Abstract} Highly specific seed market classes for cowpea and other grain legumes exist because
grain is most commonly cooked and consumed whole. Size, shape, color, and texture
are critical features of these market classes and breeders target development of cultivars
for market acceptance. Resistance to biotic and abiotic stresses that are absent from
elite breeding material are often introgressed through crosses to landraces or wild relatives.
When crosses are made between parents with different grain quality characteristics,
recovery of progeny with acceptable or enhanced grain quality is problematic.Thus genetic
markers for grain quality traits can help in pyramiding genes needed for specific market
classes. Allelic variation dictating the inheritance of seed size can be tagged and used to
assist the selection of large seeded lines. In this work we applied 1,536-plex SNP genotyping
and knowledge of legume synteny to characterize regions of the cowpea genome
associated with seed size. These marker-trait associations will enable breeders to use
marker-based selection approaches to increase the frequency of progeny with large seed.
For 804 individuals derived from eight bi-parental populations, QTL analysis was used to
identify markers linked to 10 trait determinants. In addition, the population structure of 171
samples from the USDA core collection was identified and incorporated into a genomewide
association study which supported more than half of the trait-associated regions
important in the bi-parental populations. Seven of the total 10 QTLs were supported based
on synteny to seed size associated regions identified in the related legume soybean. In
addition to delivering markers linked to major trait determinants in the context of modern
breeding, we provide an analysis of the diversity of the USDA core collection of cowpea
to identify genepools, migrants, admixture, and duplicates.